Active Transposable Elements Research Articles

Vanadium-Dependent Haloperoxidase Gene Evolution in Brown Algae: Evidence for Horizontal Gene Transfer

Compared with green plants, brown algae are characterized by their ability to accumulate iodine, contributing to their ecological adaptability in high-iodide coastal environments. Vanadium-dependent haloperoxidase (V-HPO) is the key enzyme for iodine synthesis. Despite its significance, the evolutionary origin of V-HPO genes remains underexplored. This study investigates the genomic and evolutionary dynamics of V-HPOs in brown algae, focusing on Laminariales species, particularly Saccharina japonica. Genomic analyses revealed the extensive expansion of the V-HPO gene family in brown algae, with 88 V-HPOs identified in S. japonica, surpassing the number in red algae. Phylogenetic analysis demonstrated distinct evolutionary divergence between brown and red algal V-HPOs, with the brown algal clade closely related to bacterial V-HPOs. These findings suggest horizontal gene transfer (HGT) played a key role in acquiring V-HPO genes, particularly from Acidobacteriota, a bacterial phylum known for genomic plasticity. Additionally, enriched active transposable elements were identified around V-HPO genomic clusters, highlighting their role in tandem gene duplications and rapid HGT processes. Expression profiling further revealed dynamic regulation of V-HPOs in response to environmental conditions. This study provides new insights into how HGT has driven kelp genomic adaptations and enhances understanding of marine ecological success and evolutionary processes.

Maintenance of long-term transposable element activity through regulation by nonautonomous elements.

Transposable elements are DNA sequences that can move and replicate within genomes. Broadly, there are 2 types: autonomous elements, which encode the necessary enzymes for transposition, and nonautonomous elements, which rely on the enzymes produced by autonomous elements for their transposition. Nonautonomous elements have been proposed to regulate the numbers of transposable elements, which is a possible explanation for the persistence of transposition activity over long evolutionary times. However, previous modeling studies indicate that interactions between autonomous and nonautonomous elements usually result in the extinction of one type. Here, we study a stochastic model that allows for the stable coexistence of autonomous and nonautonomous retrotransposons. We determine the conditions for this coexistence and derive an analytical expression for the stationary distribution of their copy numbers, showing that nonautonomous elements regulate stochastic fluctuations and the number of autonomous elements in stationarity. We find that the stationary variances of each element can be expressed as a function of the average copy numbers and their covariance, enabling data comparison and model validation. These results suggest that continued transposition activity of transposable elements, regulated by nonautonomous elements, is a possible evolutionary outcome that could for example explain the long coevolutionary history of autonomous LINE1 and nonautonomous Alu element transposition in the human ancestry.

Comparative genomic analysis of Fusarium oxysporum f. sp. lycopersici reveals telomeric duplications of a lineage-specific region carrying SIX8 and PSL1 and genome-wide expansion of Foxy transposable elements.

Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease, is a soil-borne, vascular-colonizing fungal pathogen that severely impacts tomato production in most growing regions worldwide. Despite the availability of over thirty Fol genome sequences in public databases, only one chromosome-scale assembly exists, comprising the low sequence-coverage Fol4287 reference genome generated using Sanger sequencing. Thus, genome structural variation and comparative genomics analyses of Fol remain largely unexplored. Here, using third generation Nanopore long-read sequencing in combination with high-throughput chromosome conformation capture (Hi-C) data, we have independently constructed a high-quality assembly and annotation of the Fol007 race 2 genome that consists of 15 pseudochromosomes with 25 telomeres, including 10 telomere-to-telomere chromosomes. The Fol007 genome is predicted to contain 29,148 protein-encoding genes, including all known SIX genes except for SIX4, which is absent in Fol race 2. Compared to the genome of Fusarium verticillioides, the Fol007 genome contains four complete lineage-specific (LS) chromosomes, including chromosome 5 (Chr5), chromosome 13 (Chr13), and two small chromosomes, Chr14 and Chr15. Comparative genomic analysis between the newly assembled Fol007 genome and Fol4287_2010 deposited in the GenBank database reveals that the completely assembled Chr13 of Fol007 carrying all known SIX genes (except SIX4 and SIX8) and three novel candidate effector genes is relatively stable and corresponds to pathogenicity chromosome Chr14 in Fol4287_2010. It also reveals a telomeric duplication of an LS region carrying SIX8 and PSL1 on core chromosomes Chr6, Chr7 and Chr11, and LS chromosome Chr15, as well as the absence of segmental duplications on LS chromosomes of the Fol007 genome. Furthermore, compared to the genomes of Fol race 1 and non-pathogenic Fo strains, an active and specific Foxy transposable element, responsible for the inactivation of a second copy of SIX13, was identified and found to have expanded in the genomes of Fol race 2 and 3 strains. This element may contribute to Fusarium oxysporum genome evolution and has potential as a genetic marker for studying phylogenetic relationships among formae speciales of Fusarium oxysporum. These findings provide a basis for further genetic and genomic understanding of Fol evolution and virulence mechanisms employed by Fol and contribute another reference genome for Fusarium study more broadly.

The role of mobile DNA elements in the dynamic of plants genome plasticity.

Plants host a range of DNA elements capable of self-replication. These molecules, usually associated to the activity of transposable elements or viruses, are found integrated in the genome or in the form of extrachromosomal DNA. The activity of these elements can impact genome plasticity by a variety of mechanisms, including the generation of structural variants, the shuffling of regulatory or coding DNA sequences across the genome, and DNA endoduplication. This plasticity can dynamically alter gene expression and genome stability, ultimately affecting plant development or the response to environmental changes. While the activation of these elements is often considered deleterious to the genome, their role in creating variation is important in adaptation and evolution. Moreover, the mechanisms by which mobile DNA proliferate have been exploited for plant engineering, or contributed to understand how desirable traits can be generated in crops. In this review, we discuss the origins and the roles of mobile DNA element activity on genome plasticity and plant biology, as well as their potential function and current application in plant biotechnology.

Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.

Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within and among species, as well as the roles of host genes and non-coding RNAs in the transposition process, remain elusive. With advancements in large-scale pan-genome sequencing and the development of open data sharing, large-scale comparative genomics studies have become feasible. Here, we performed complete de novo TE annotations and identified active TEs in 310 plant genome assemblies across 119 species and seven crop populations. Using 811 high-quality genomes, we detected 13 844 553 TE-induced structural variants (TE-SVs), providing unprecedented resolution in delineating recent TE activities. Our integrative analysis revealed a mutual evolutionary relationship between TEs and host genomes. On one hand, host genes and ncRNAs are involved in the transposition process, as evidenced by their colocalization and coactivation with TEs, and may play a role in chromatin regulation. On the other hand, TEs drive genetic innovation by promoting the duplication of host genes and inserting into regulatory regions. Moreover, genes influenced by active TEs are linked to plant growth, nutrient absorption, storage metabolism and environmental adaptation, aiding in crop domestication and adaptation. This TE dynamics atlas not only reveals evolutionary and functional features linked to transposition activity but also highlights the role of TEs in crop domestication and adaptation, paving the way for future exploration of TE-mediated genome evolution and crop improvement strategies.

A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex.

Somatic mutations in individual cells lead to genomic mosaicism, contributing to the intricate regulatory landscape of genetic disorders and cancers. To evaluate and refine the detection of somatic mosaicism across different technologies with personalized donor-specific assembly (DSA), we obtained tissue from the dorsolateral prefrontal cortex (DLPFC) of a post-mortem neurotypical 31-year-old individual. We sequenced bulk DLPFC tissue using Oxford Nanopore Technologies (~60X), NovaSeq (~30X), and linked-read sequencing (~28X). Additionally, we applied Cas9 capture methodology coupled with long-read sequencing (TEnCATS), targeting active transposable elements. We also isolated and amplified DNA from flow-sorted single DLPFC neurons using MALBAC, sequencing 115 of these MALBAC libraries on Nanopore and 94 on NovaSeq. We constructed a haplotype-resolved assembly with a total length of 5.77 Gb and a phase block length of 2.67 Mb (N50) to facilitate cross-platform analysis of somatic genetic variations. We observed an increase in the phasing rate from 11.6% to 38.0% between short-read and long-read technologies. By generating a catalog of phased germline SNVs, CNVs, and TEs from the assembled genome, we applied standard approaches to recall these variants across sequencing technologies. We achieved aggregated recall rates from 97.3% to 99.4% based on long-read bulk tissue data, setting an upper bound for detection limits. Moreover, utilizing haplotype-based analysis from DSA, we achieved a remarkable reduction in false positive somatic calls in bulk tissue, ranging from 14.9% to 72.4%. We developed pipelines leveraging DSA information to enhance somatic large genetic variant calling in long-read single cells. By examining somatic variation using long-reads in 115 individual neurons, we identified 468 candidate somatic heterozygous large deletions (1.5Mb - 20Mb), 137 of which intersected with short-read single-cell data. Additionally, we identified 61 putative somatic TEs (60 Alus, one LINE-1) in the single-cell data. Collectively, our analysis spans personalized assembly to single-cell somatic variant calling, providing a comprehensive ab initio ad finem approach and resource in real human tissue.

DNA Damage, Transposable Element Expression and Their Associated Factors in Aging

Aging is a spontaneous and permanent physiological process that leads to declines in tissue and cell functions, along with an increased risk of developing various age-related diseases. The primary driving force associated with aging is the accumulation of damaged genetic material in the cell, such as DNA. DNA damage can be caused by endogenous and exogenous factors, which leads to genome instability, mitochondrial dysfunction, epigenetic modifications, and proteostatic disturb. Another driving force associated with aging is the disruption of cellular metabolism. This disruption is closely linked to alterations in the role of metabolic pathways, including insulin/IGF-1 and mTOR, which regulate crucial cellular processes like cell growth, cell proliferation, and apoptosis. The activation of the insulin/IGF-1 signaling pathway highly promotes cell growth and proliferation, while also inhibits autophagy and increasing ROS production. This ultimately leads to accelerated aging. Another crucial signaling pathway is the mTOR signaling pathway. It is responsible for detecting nutrient availability and controlling cell growth and metabolism. The dysregulation of mTOR function can lead to the development of neurodegenerative diseases, which are characterized by the aggregation of protein. Activation of transposable elements is the other driving force of aging, caused by changes in DNA methylation and the loss of heterochromatin. As a result, this leads to DNA damage, genomic instability, and inflammation. The aim of this review is to elucidate the consequence of DNA damage and other associated factors drive aging.

Potential impacts of AluYa5 (ACE & PROGINS) and AluYb8 (MUTYH) insertions in panic disorder

Objective: The human genome contains numerous active transposable elements (TEs), including the inserts of young Alus such as AluYa5 and AluYb8. The rapid, human lineage-specific evolution of brain size may be influenced by natural selection and the genomic variation of TEs, which can act as catalysts of evolution. Given their potential effects on human brain development, Alu elements may also be relevant in exploring complementary approaches for psychiatric disorders. This study analyzed the potential impacts of three specific Alu insertions (AluYa5-ACE, AluYa5-PROGINS, and AluYb8-MUTYH) on the susceptibility to panic disorder (PD). Materials and Methods: Alu insertions were determined with Polymerase Chain Reaction (PCR) method in 120 PD patients and 120 healthy control individuals and analyzed with logistic regression. The associations of the investigated Alus with both categorical and quantitative demographic-clinical variables including the Panic Disorder Severity Scale (PDSS) were analyzed using Fisher's exact and Kruskal-Wallis tests. Results: AluYa5-PROGINS and AluYb8-MUTYH did not show an association with panic disorder risk. For AluYa5-ACE, a statistically significant association was determined; logistic regression analysis proved the highly protective effect (47.9%) of I/D genotype against PD compared with D/D genotype (p=0.030, OR=0.521, 95% CI=0.290-0.937). Alu insertions were not associated with panic disorder severity (p>0.05). Conclusion: This is the first combined study in which the potential effects of three Alu insertions in terms of both PD susceptibility and possible association with several disease parameters were evaluated. Further studies about the roles of the Alu elements in the etiology PD are highly recommended.

Termites and other social insects as emerging model organisms of ageing research: how to achieve a long lifespan and a high fecundity.

Social insects (termites, ants and some bees and wasps) are emerging model organisms of ageing research. In this Commentary, I outline which advantages they offer compared with other organisms. These include the co-occurrence of extraordinarily long-lived, highly fecund queens together with short-lived workers within colonies that share the same genetic background. I then summarize which new insights have been gained so far from social insect studies. Research on social insects has led to the development of a universal mechanistic framework underlying the regulation of ageing and other life-history trade-offs in insects: the TI-J-LiFe network (short for TOR/IIS-juvenile hormone-lifespan/fecundity). Because of its conservative nature, this network can be extended to also incorporate vertebrates. Current data for social insect models suggest that molecular re-wirings along the I-J-Fe (IIS-juvenile hormone-fecundity) axis of the network can explain the concurrent long lifespans and high fecundity of queens. During social evolution, pathways that foster a high fecundity have apparently been uncoupled from mechanisms that shorten lifespan in solitary insects. Thus, fecundity-related vitellogenesis is uncoupled from life-shortening high juvenile hormone (JH)-titres in the honeybee and from insulin/insulin-like growth factor signalling (IIS) activity in ants. In termites, similarly, vitellogenesis seems tissue-specifically unlinked from JH signalling and IIS activity might have lost life-shortening consequences. However, as in solitary animals, the downstream processes (Li of the TI-J-LiFe network) that cause actual ageing (e.g. oxidative stress, transposable element activity, telomere attrition) seem to differ between species and environments. These results show how apparently hard-wired mechanisms underlying life-history trade-offs can be overcome during evolution.

Single cell long read whole genome sequencing reveals somatic transposon activity in human brain.

The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover novel dynamics in three brains utilizing single cell long-read sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements.

Characterization of the enzyme for 5-hydroxymethyluridine production and its role in silencing transposable elements in dinoflagellates

Dinoflagellate chromosomes are extraordinary, as their organization is independent of architectural nucleosomes unlike typical eukaryotes and shows a cholesteric liquid crystal state. 5-hydroxymethyluridine (5hmU) is present at unusually high levels and its function remains an enigma in dinoflagellates chromosomal DNA for several decades. Here, we demonstrate that 5hmU contents vary among different dinoflagellates and are generated through thymidine hydroxylation. Importantly, we identified the enzyme, which is a putative dinoflagellate TET/JBP homolog, catalyzing 5hmU production using both in vivo and in vitro biochemical assays. Based on the near-chromosomal level genome assembly of dinoflagellate Amphidinium carterae, we depicted a comprehensive 5hmU landscape and found that 5hmU loci are significantly enriched in repeat elements. Moreover, inhibition of 5hmU via dioxygenase inhibitor leads to transcriptional activation of 5hmU-marked transposable elements, implying that 5hmU appears to serve as an epigenetic mark for silencing transposon. Together, our results revealed the biogenesis, genome-wide landscape, and molecular function of dinoflagellate 5hmU, providing mechanistic insight into the function of this enigmatic DNA mark.

PTGS is dispensable for the initiation of epigenetic silencing of an active transposon in Arabidopsis

Transposable elements (TEs) are repressed in plants through transcriptional gene silencing (TGS), maintained epigenetic silencing marks such as DNA methylation. However, the mechanisms by which silencing is first installed remain poorly understood in plants. Small interfering (si)RNAs and post-transcriptional gene silencing (PTGS) are believed to mediate the initiation of TGS by guiding the first deposition of DNA methylation. To determine how this silencing installation works, we took advantage of ÉVADÉ (EVD), an endogenous retroelement in Arabidopsis, able to recapitulate true de novo silencing with a sequence of PTGS followed by a TGS. To test whether PTGS is required for TGS, we introduce active EVD into RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) mutants, an essential PTGS component. EVD activity and silencing are monitored across several generations. In the absence of PTGS, silencing of EVD is still achieved through installation of RNA-directed DNA methylation (RdDM). Our study shows that PTGS is dispensable for de novo EVD silencing. Although we cannot rule out that PTGS might facilitate TGS, or control TE activity, initiation of epigenetic silencing can take place in its absence.

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei.

The coffee berry borer (CBB) Hypothenemus hampei was first described in Africa in 1867 and has spread to all major coffee-producing regions worldwide, including Jamaica. Using long-read sequencing, we produced a new high-quality reference genome (172.7 Mb) for the Jamaican strain of the CBB, with 93% of the genome assembled into 14 scaffolds. Whole genome sequencing of pooled samples from different populations across Jamaica showed that the CBB harbors low levels of genetic diversity alongside an excess of low-frequency alleles, indicative of a recent genetic bottleneck. The analyses also showed a recent surge in the activity of transposable elements (TEs), particularly LINE/R1 and LTR/Gypsy elements, within CBB populations. Our findings offer first insights into the evolutionary genomics of CBB populations in Jamaica, highlighting the potential role of TEs in shaping the genome of this important pest species.

Transposable Element Diversity and Activity Patterns in Neotropical Salamanders.

Transposable elements (TEs) compose a substantial proportion of the largest eukaryotic genomes. TE diversity has been hypothesized to be negatively correlated with genome size, yet empirical demonstrations of such a relationship in a phylogenetic context are largely lacking. Furthermore, the most abundant type of TEs in genomes varies across groups, and it is not clear if there are patterns of TE activity consistent with genome size among different taxa with large genome sizes. We use low-coverage sequencing of 16 species of Neotropical salamanders, which vary ∼7-fold in genome size, to estimate TE relative abundance and diversity for each species. We also compare the divergence of copies of each TE superfamily to estimate patterns of TE activity in each species. We find a negative relationship between TE diversity and genome size, which is consistent with the hypothesis that either competition among TEs or reduced selection against ectopic recombination may result in lower diversity in the largest genomes. We also find divergent activity patterns in the largest versus the smallest genomes, suggesting that the history of TE activity may explain differences in genome size. Our results suggest that both TE diversity and relative abundance may be predictable, at least within taxonomic groups.

YY1 is a transcriptional activator of the mouse LINE-1 Tf subfamily.

Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element in human and mouse genomes. L1 transcription is controlled by an internal RNA polymerase II promoter in the 5' untranslated region (5'UTR) of a full-length L1. It has been shown that transcription factor YY1 binds to a conserved sequence at the 5' end of the human L1 5'UTR and primarily dictates where transcription initiates. Putative YY1-binding motifs have been predicted in the 5'UTRs of two distinct mouse L1 subfamilies, Tf and Gf. Using site-directed mutagenesis, in vitro binding and gene knockdown assays, we experimentally tested the role of YY1 in mouse L1 transcription. Our results indicate that Tf, but not Gf subfamily, harbors functional YY1-binding sites in 5'UTR monomers and YY1 functions as a transcriptional activator for the mouse Tf subfamily. Activation of Tf transcription by YY1 during early embryogenesis is also supported by a reanalysis of published zygotic knockdown data. Furthermore, YY1-binding motifs are solely responsible for the synergistic interaction between Tf monomers, consistent with a model wherein distant monomers act as enhancers for mouse L1 transcription. The abundance of YY1-binding sites in Tf elements also raise important implications for gene regulation across the genome.

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew.

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens.

Transposable elements as drivers of dedifferentiation: Connections between enhancers in embryonic stem cells, placenta, and cancer.

Transposable elements (TEs) have emerged as important factors in establishing the cell type-specific gene regulatory networks and evolutionary novelty of embryonic and placental development. Recently, studies on the role of TEs and their dysregulation in cancers have shed light on the transcriptional, transpositional, and regulatory activity of TEs, revealing that the activation of developmental transcriptional programs by TEs may have a role in the dedifferentiation of cancer cells to the progenitor-like cell states. This essay reviews the recent evidence of the cis-regulatory TEs (henceforth crTE) in normal development and malignancy as well as the key transcription factors and regulatory pathways that are implicated in both cell states, and presents existing gaps remaining to be studied, limitations of current technologies, and therapeutic possibilities.

Transposon-mediated genic rearrangements underlie variation in small RNA pathways

Transposable elements (TEs) can alter host gene structure and expression, whereas host organisms develop mechanisms to repress TE activities. In the nematode Caenorhabditis elegans , a small interfering RNA pathway dependent on the helicase ERI-6/7 primarily silences retrotransposons and recent genes of likely viral origin. By studying gene expression variation among wild C. elegans strains, we found that structural variants and transposon remnants likely underlie expression variation in eri-6/7 and the pathway targets. We further found that multiple insertions of the DNA transposons, Polintons, reshuffled the eri-6/7 locus and induced inversion of eri-6 in some wild strains. In the inverted configuration, gene function was previously shown to be repaired by unusual trans-splicing mediated by direct repeats. We identified that these direct repeats originated from terminal inverted repeats of Polintons . Our findings highlight the role of host-transposon interactions in driving rapid host genome diversification among natural populations and shed light on evolutionary novelty in genes and splicing mechanisms.

Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants.

The naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g. polyploidy, engorged nutritional rewards, and dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g. plant fragment degradation, ant-farmer communication, and antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: (i) free-living to ant-cultivated: loss of genes conferring stress response and detoxification; (ii) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis; and (iii) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by 3 leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes toward long-term ecological resilience of farming systems that have thrived across millennia.

Characterization of active transposable elements and their new insertions in tuber propagated greater yam (Dioscorea alata)

BackgroundGreater yam is a key staple crop grown in tropical and subtropical regions, while its asexual propagation mode had led to non-flowering mutations. How transposable elements contribute to its genetic variations is rarely analyzed. We used transcriptome and whole genome sequencing data to identify active transposable elements (TEs) and genetic variation caused by these active TEs. Our aim was to shed light on which TEs would lead to its intraspecies variation.ResultsAnnotation of de novo assembly transcripts indicated that 0.8 − 0.9% of transcripts were TE related, with LTR retrotransposons (LTR-RTs) accounted for 65% TE transcripts. A large portion of these transcripts were non-autonomous TEs, which had incomplete functional domains. The majority of mapped transcripts were distributed in genic deficient regions, with 9% of TEs overlapping with genic regions. Moreover, over 90% TE transcripts exhibited low expression levels and insufficient reads coverage to support full-length structure assembly. Subfamily analysis of Copia and Gypsy, the two LTR-RTs revealed that a small number of subfamilies contained a significantly larger number of members, which play a key role in generating TE transcript. Based on resequencing data, 15,002 L-RT insertion loci were detected for active LTR-RT members. The insertion loci of LTR-RTs were highly divergent among greater yam accessions.ConclusionsThis study showed the ongoing transcription and transpositions of TEs in greater yam, despite low transcription levels and incomplete proteins insufficient for autonomous transposition. While our research did not directly link these TEs to specific yam traits such as tuber yield and propagation mode, it lays a crucial foundation for further research on how these TE insertion polymorphisms (TIPs) might be related to variations in greater yam traits and its tuber propagation mode. Future research may explore the potential roles of TEs in trait variations, such as tuber yield and stress resistance, in greater yam.